{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd .."
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mkdir Test"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd Test/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace/Test\n"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd .."
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace\n"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd epitopsy/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace/epitopsy\n"
       ]
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import Bio"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ls"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "APBS.py                   build_cython.py   \u001b[0m\u001b[01;34mcython\u001b[0m/    \u001b[01;34mfunctions\u001b[0m/   \u001b[01;34mOptimization\u001b[0m/  \u001b[01;34mscoring\u001b[0m/     Structure.py  Untitled0.ipynb\r\n",
        "build_cython_cluster.py~  build_cython.py~  DXFile.py  __init__.py  \u001b[01;34mresult\u001b[0m/        Sequence.py  \u001b[01;34mtools\u001b[0m/\r\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd functions/"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace/epitopsy/functions\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "l"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "NameError",
       "evalue": "name 'l' is not defined",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-11-12f54a96f644>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0ml\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;31mNameError\u001b[0m: name 'l' is not defined"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ls"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "CalculateESPProfiles.py                 CreateHull.py                                     ESP_Profile_SurfacePatch.py  StartMD.py\r\n",
        "Calculate_Ligand_Interaction_Energy.py  depreciated_calculate_partition_function_slow.py  __init__.py\r\n",
        "calculate_partition_function.py         ESP_Profile_Extract_SurfacePatch.py               ScoreHullEnsemble.py\r\n",
        "CreateHullEnsemble.py                   ESP_Profile_Extract_Volume.py                     ScoreHull.py\r\n"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd ../.."
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "/home/ludwig/workspace\n"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import epitopsy"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 14
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import sys"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "sys.path"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 16,
       "text": [
        "['',\n",
        " '/home/ludwig/anaconda/lib/python27.zip',\n",
        " '/home/ludwig/anaconda/lib/python2.7',\n",
        " '/home/ludwig/anaconda/lib/python2.7/plat-linux2',\n",
        " '/home/ludwig/anaconda/lib/python2.7/lib-tk',\n",
        " '/home/ludwig/anaconda/lib/python2.7/lib-old',\n",
        " '/home/ludwig/anaconda/lib/python2.7/lib-dynload',\n",
        " '/home/ludwig/anaconda/lib/python2.7/site-packages',\n",
        " '/home/ludwig/anaconda/lib/python2.7/site-packages/PIL',\n",
        " '/home/ludwig/anaconda/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info',\n",
        " '/home/ludwig/anaconda/lib/python2.7/site-packages/IPython/extensions']"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import epi"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 17
    }
   ],
   "metadata": {}
  }
 ]
}